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Backport fix from PR #542 #543

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Merged
lohedges merged 1 commit into from
Jul 29, 2026
Merged

Backport fix from PR #542 #543

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8 changes: 4 additions & 4 deletions src/BioSimSpace/Align/_merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1589,10 +1589,10 @@ def _check_ring(conn0, conn1, idx0, idy0, idx1, idy1, max_path=50, max_ring_size
# Supplementary check for rings larger than max_path: find_paths may only
# find the direct-bond path and miss the long way around the ring, giving
# n=1 instead of n≥2. Sire's in_ring has no path-length limit and
# correctly identifies ring membership in macrocycles.
if (conn0.in_ring(idx0) and conn0.in_ring(idy0)) != (
conn1.in_ring(idx1) and conn1.in_ring(idy1)
):
# correctly identifies ring membership in macrocycles. The two-atom
# overload asks whether the atoms share a ring, so a ring built entirely
# from dummy atoms, which breaks no bond between mapped atoms, is ignored.
if conn0.in_ring(idx0, idy0) != conn1.in_ring(idx1, idy1):
return True, False

# A direct bond was replaced by a ring path (or vice versa), leaving the
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8 changes: 4 additions & 4 deletions src/BioSimSpace/Sandpit/Exscientia/Align/_merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1455,10 +1455,10 @@ def _check_ring(conn0, conn1, idx0, idy0, idx1, idy1, max_path=50, max_ring_size
# Supplementary check for rings larger than max_path: find_paths may only
# find the direct-bond path and miss the long way around the ring, giving
# n=1 instead of n≥2. Sire's in_ring has no path-length limit and
# correctly identifies ring membership in macrocycles.
if (conn0.in_ring(idx0) and conn0.in_ring(idy0)) != (
conn1.in_ring(idx1) and conn1.in_ring(idy1)
):
# correctly identifies ring membership in macrocycles. The two-atom
# overload asks whether the atoms share a ring, so a ring built entirely
# from dummy atoms, which breaks no bond between mapped atoms, is ignored.
if conn0.in_ring(idx0, idy0) != conn1.in_ring(idx1, idy1):
return True, False

# A direct bond was replaced by a ring path (or vice versa), leaving the
Expand Down